Problem mixing a scene with video clips in the VSE
The main output of Blender is the 3D window, after that you must activate the Compositor to apply effects (like color grade or blur) by checking the Compositor box in the Scene Properties panel. Then you can bring that compositor output (or the 3D scene) into the VSE for editing with other footage (as you have done). But for this render engine to work you must check the Sequencer (as in Video Sequence Editor) box. 

Note that you can check either or both the Compositor or the Sequencer box, depending on what functions you want.

If you only want to edit video clips or pre-rendered animations, then you MUST check the Sequencer box, otherwise the VSE output will not be rendered. In fact all you will see is what is present in the 3D view.